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The Virtual Brain Simulation Platform

Purpose of the study track
The Virtual Brain takes a network approach on the largest scale: By manipulating network parameters, in particular the brain’s connectivity, The Virtual Brain simulates its behavior as it is commonly observed in clinical scanners (e.g. EEG, MEG, fMRI).

About The Virtual Brain Simulation Platform: 

The Virtual Brain takes a network approach on the largest scale: By manipulating network parameters, in particular the brain’s connectivity, The Virtual Brain simulates its behavior as it is commonly observed in clinical scanners (e.g. EEG, MEG, fMRI). Though The Virtual Brain incorporates the complex world of neuro-chemistry only to a small degree, it gains a lot by not becoming as complex as the brain itself. Instead, The Virtual Brain embraces and extends novel concepts from computational, cognitive and clinical neuroscience in order to drastically reduce the model's complexity while still keeping it sufficiently realistic – and delivering the same output as clinical brain-scanners.

1

In this short series of lectures, participants will take a look at articles using TVB in a clinical context. Specifically, participants will see how TVB can help to predict recovery after stroke and how individual epileptic seizures are simulated. The course lecturers will briefly describe the methods used and results achieved in the articles. Using the graphical user interface, participants will replicate the principle ideas of the articles and see how artificial lesions introduced in the connectome alter brain dynamics, as well es how seizures spreading through the brain network can be modelled. All videos are using the default TVB dataset, such that you can follow along each step in your own TVB GUI.

2

This course provides a general overview about brain simulation, its fundamentals and clinical applications in stroke, neurodegeneration, epilepsy and brain tumors. The mathematical framework of multi-scale brain modeling and its analysis is introduced. In particular, you get to know the open-source neuroinfromatcis platform The Virtual Brain and learn how to use it in the graphical user interface and by pythons scripts. In the end, you can create your own epilepsy brain simulations. The lectures were originally given in the Bernstein Center of Computational Neuroscience in Berlin in April 2019.

3

Get up to speed about the fundamental principles of full brain network modeling using the open-source neuroinformatics platform The Virtual Brain (TVB). This simulation environment enables the biologically realistic modeling of whole-brain network dynamics across different brain scales, using personalized structural connectome-based approach. Configurable brain network models generate macroscopic neuroimaging signals including functional MRI, intracranial and stereotactic EEG, surface EEG and MEG for single subjects. Researchers from different backgrounds can benefit from an integrative software platform including a simulation core written in Python and a supporting framework for data management (generation, organization, storage, integration and sharing).

The workshop is dedicated to a theoretical and practical understanding of large-scale brain network modeling using the open-source neuroinformatics platform The Virtual Brain (TVB).

4

TVB EduPack (1) provides didactic use cases for The Virtual Brain. Typically a use case consists of a jupyter notebook and a didactic video. EduPack use cases help the user to reproduce TVB based publications or to get started quickly with TVB. EduCases demonstrate for example how to use TVB via the Collaboratory of the Human Brain Project, how to run multi-scale co-simulations with other simulators such as NEST, how to process imaging data to construct personalized virtual brains of healthy individuals and patients.